Li Fraumeni Syndrome
GTR Test Accession: Help GTR000210160.4
CANCERINHERITED DISEASEINHERITED DISEASE SUSCEPTIBILITY ... View more
Last updated in GTR: 2024-02-07
Last annual review date for the lab: 2024-02-07 LinkOut
At a Glance
Diagnosis; Mutation Confirmation; Pre-symptomatic; ...
Li-Fraumeni syndrome; Breast cancer, early-onset; Breast cancer, familial male more...
Genes (1): Help
TP53 (17p13.1)
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Not provided
It is estimated that 80% of families with LFS will …
Establish or confirm diagnosis; Predictive risk information for patient and/or family members
Ordering Information
Offered by: Help
Molecular Genetics Laboratory
View lab's website
View lab's test page
Test short name: Help
p53
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Licensed Physician
Test Order Code: Help
Li Fraumeni Syndrome (p53)
Lab contact: Help
Gavin Giles, MSc, Administrator
gavin.giles@lhsc.on.ca
+1-519-685-8500 x36339
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
Please complete the requisition found on our website and sign and submit with the appropriate sample. See shipping instructions for further details
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Test additional service: Help
Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required: Help
Decline to answer
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Conditions Help
Total conditions: 5
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 1
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 3
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina MiSeq/NextSeq
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Applied Biosystems 3730 capillary sequencing instrument
Illumina MiSeq/NextSeq
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic; Predictive; Risk Assessment
Clinical validity: Help
It is estimated that 80% of families with LFS will harbour an identifiable TP53 mutation.
View citations (1)
  • Li-fraumeni syndrome. Malkin D, et al. Genes Cancer. 2011;2(4):475-84. doi:10.1177/1947601911413466. PMID: 21779515.
Clinical utility: Help
Establish or confirm diagnosis

Predictive risk information for patient and/or family members

Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
Novel variations are interrogated using a series of tools. Literature reviews and a search of relevant databases and dbSNP is pursued. This is followed by evaluation using web based insilco analysis including, but not restricted to SIFT, Polyphen2, AlignGVGD, SNPs&GO and ASSEDA(splice). If the pathogenicity is still indeterminate (ACMG group … View more

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Not provided.
Recommended fields not provided:
Technical Information
Test Procedure: Help
All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations in a single assay that … View more
View citations (1)
  • Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Test Confirmation: Help
All positive results and known familial mutations are confirmed by a second independent method
Test Comments: Help
Direct sequence of all coding exons
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
The LHSC NGS protocol is predicted to detect in excess of 99% of mutations present within the genes listed. Mutation detection rates in the patient are dependent on the clinical presentation including age of onset, specific diagnostic features, and family history.
View citations (1)
  • Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
No
VUS:
Software used to interpret novel variations Help
ALAMUT, integrating other programs (Polyphen-2, Mutation Taster, Alignment, ExPASy, BLAST)

Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: Not Applicable
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.